They were still having sex right up until three days before she left town. So she has had plenty of time to bake a wheat bun, and have it walking and talking in another town. Just like Val did when she returned to Salem the second time, she did not bring little Eli with her. And on her third return no one even knew she had a son until Eli showed up. It is very possible for Jordan to return to Salem without a child in tow, but still have one in NYC being cared for by a friend or nanny.
He did care that she was leaving - YouTube it.
Okay, in order to save myself some time, let me just say I know why Jordan is returning and it's not to surprise Chad with a baby.